/// <summary>
/// Execute the workflow
/// </summary>
public virtual void Execute()
{
try
{
InitializeWorkflow();
}
catch (Exception ex)
{
var simpleErrorMessage = "Error - during workflow initialization. Internal error message: " + ex.Message;
LogError(ex, simpleErrorMessage);
throw new ApplicationException(simpleErrorMessage, ex);
}
WorkflowStats = new WorkflowStats
{
TimeStarted = DateTime.Now
};
try
{
IterateOverScans();
}
catch (Exception ex)
{
var simpleErrorMessage = "A bad error happened while processing each scan in the dataset. Internal error message: " + ex.Message;
LogError(ex, simpleErrorMessage);
throw new ApplicationException(simpleErrorMessage, ex);
}
WorkflowStats.TimeFinished = DateTime.Now;
WorkflowStats.NumFeatures = Run.ResultCollection.MSFeatureCounter;
WriteOutSummaryToLogfile();
}
private void IterateOverDatasets()
{
_datasetCounter = 0;
_peaksProcessedInLastDataset = 0;
_totalPeaksProcessed = 0;
WorkflowStats = new WorkflowStats
{
TimeStarted = DateTime.UtcNow
};
foreach (var datasetFileName in DatasetFileNameList)
{
_peaksProcessedInLastDataset = 0;
Run = new RunFactory().CreateRun(datasetFileName);
Check.Require(Run != null, "ERROR: tried to initialize Run but failed.");
if (_datasetCounter == 0)
{
InitializeWorkflow();
}
CreateTargetMassSpectra();
IterateOverScans();
_totalPeaksProcessed += _peaksProcessedInLastDataset;
_datasetCounter++;
}
WorkflowStats.TimeFinished = DateTime.UtcNow;
WorkflowStats.NumFeatures = _totalPeaksProcessed;
WriteOutSummaryToLogfile();
}